tisdag 8 oktober 2013

http://phys.org/news/2013-05-database-phosphate-substrate.html
It is now easier to pinpoint exactly what molecules a phosphatase –
a type of protein that's essential for cells to react to their
environment – acts upon in human cells, thanks to the free online
database DEPOD, created by EMBL scientists. Published today in Science Signaling, the overview of interactions could even help explain unforeseen side-effects of drugs.

Although we know the tool's general purpose, it can sometimes
be difficult to tell if a specific pair of precision tweezers belongs
to a surgeon or a master jeweller. It is now easier to solve similar
conundrums about a type of protein that allows cells to react to their
environment, thanks to scientists at the European Molecular Biology
Laboratory (EMBL). Published today in Science Signaling, their work offers a valuable resource for other researchers.
Whether in your eye being hit by light, in your blood fighting off
disease, or elsewhere throughout your body, cells have to react to
changes in their environment. But first, a cell must 'know' the
environment has changed. One of the ways in which that information is
transmitted within the cell is through tags called phosphate ions,which
are added to or removed from specific molecules depending on the exact
message that has to be conveyed. The tools the cell uses to remove
phosphate ions are proteins called phosphatases. But it's not always
obvious what molecules – or substrates – a particular phosphatase acts
upon.
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"One of the biggest
challenges in phosphatase research is finding substrates, and this is
what our work supports," says Maja Köhn from EMBL in Heidelberg,
Germany, who led the study. "We've made it easier to create hypotheses
about the relationships between phosphatases and their substrates."
Xun Li, a post-doctoral student shared by Köhn's lab and those of
Matthias Wilmanns at EMBL in Hamburg, Germany and Janet Thornton at
EMBL-European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK,
compiled the most complete picture to date of all the phosphatases in human cells,
and their substrates. The scientists also grouped phosphatases into
families, based on their three-dimensional structure, which can
influence what molecules a phosphatase can act upon.
This information allows researchers to easily identify a
phosphatase's known substrates, and suggest new substrates based on how
similar it is to other phosphatases. The web-like overview of
interactions could even help explain unforeseen side-effects of drugs
designed to interfere with phosphatases or with their phosphate-adding
counterparts, kinases. To enable others to make such connections, Köhn
and colleagues have created a free online database, DEPOD.
"When people have unexpected results, this could be a place to find
explanations," says Thornton, head of EMBL-EBI. "DEPOD combines a wealth
of information that can be explored in a variety of ways, to make it
useful not just to phosphatase researchers but to the wider community."

"One of the biggest
challenges in phosphatase research is finding substrates, and this is
what our work supports," says Maja Köhn from EMBL in Heidelberg,
Germany, who led the study. "We've made it easier to create hypotheses
about the relationships between phosphatases and their substrates."
Xun Li, a post-doctoral student shared by Köhn's lab and those of
Matthias Wilmanns at EMBL in Hamburg, Germany and Janet Thornton at
EMBL-European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK,
compiled the most complete picture to date of all the phosphatases in human cells,
and their substrates. The scientists also grouped phosphatases into
families, based on their three-dimensional structure, which can
influence what molecules a phosphatase can act upon.
This information allows researchers to easily identify a
phosphatase's known substrates, and suggest new substrates based on how
similar it is to other phosphatases. The web-like overview of
interactions could even help explain unforeseen side-effects of drugs
designed to interfere with phosphatases or with their phosphate-adding
counterparts, kinases. To enable others to make such connections, Köhn
and colleagues have created a free online database, DEPOD.
"When people have unexpected results, this could be a place to find
explanations," says Thornton, head of EMBL-EBI. "DEPOD combines a wealth
of information that can be explored in a variety of ways, to make it
useful not just to phosphatase researchers but to the wider community."

Triphosphates are salts or esters of polymeric oxyanions formed from tetrahedral PO4 (phosphate)
structural units linked together by sharing oxygen atoms. When two
corners are shared the polyphosphate may have a linear chain structure
or a cyclic ring structure. In biology the polyphosphate esters AMP, ADP and ATP
are involved in energy transfer. A variety of polyphosphates find
application in mineral sequestration in municipal waters, generally
being present at 1 to 5 pm.[1]GTP, CTP, and UTP are also nucleotides important in the protein synthesis, lipid synthesis and carbohydrate metabolism, respectively.

Structure & Formation

The structure of tripolyphosphoric acid illustrates the principles
which define the structures of polyphosphates. It consists of three
tetrahedral PO4 units linked together by sharing oxygen
atoms. Structurally, the outer tetrahedra share one vertex with the
central tetrahedron; the central tetrahedron shares two corners with the
other tetrahedra. The corresponding phosphates are related to the acids
by loss of the acidic protons. In the case of the cyclic trimer each tetrahedron shares two vertices with adjacent tetrahedra.
Sharing of three corners is possible as in the sheet-structure Phyllosilicates, but such structures occur only under extreme conditions. Three-corner sharing also occurs in phosphorus pentoxide, P4O10, which has a 3-dimensional structure.
Chemically, the polymerization reaction can be seen as a condensation
reaction. The process begins with two phosphate units coming together.

2 PO43− + 2 H+ P2O74− + H2O

It is shown as an equilibrium reaction because it can go in the reverse direction, when it is known as an hydrolysis reaction because a water molecule is split (Lysed). The process may continue in steps; at each step another PO3 unit is added to the chain, as indicated by the part in brackets in the illustration of polyphosphoric acid. P4O10
can be seen as the end product of condensation reactions, where each
tetrahedron shares three corners with the others. Conversely, a complex
mix of polymers is produced when a small amount of water is added to
phosphorus pentoxide.

Acid-base and complexation properties

Polyphosphates are weak bases. A lone pair of electrons on an oxygen atom can be donated to a hydrogen ion (proton) or a metal ion in a typical Lewis acid-Lewis base
interaction. This has profound significance in biology. For instance,
adenosine triphosphate (ATP) is about 25% protonated in aqueous solution at
pH 7.[2]

ATP4- + H+ ATPH3-, pKa 6.6

Further protonation occurs at lower pH values.
ATP forms chelate complexes with metal ions. The stability constant for the equilibrium

ATP4- + Mg2+ MgATP2-, log β 4

is particularly large.[3]
The formation of the magnesium complex is a critical element in the
process of ATP hydrolysis, as it weakens the link between the terminal
phosphate group and the rest of the molecule.[2][4]

The "high energy" phosphate bond

The energy released in ATP hydrolysis,

ATP4- + H2O → ADP3- + Pi-

at ΔG -36.8 kJ mol−1 is large by biological standards. Pi
stands for inorganic phosphate, which is protonated at biological pH.
However, it is not large by inorganic standards. The term "high energy"
refers to the fact that it is high relative to the amount of energy
released in the organic chemical reactions that can occur in living systems.

High-polymeric inorganic polyphosphates

High-polymeric inorganic polyphosphates were found in living
organisms by L. Liberman in 1890. These compounds are linear polymers
containing a few to several hundred residues of orthophosphate linked by energy-rich phosphoanhydride bonds.
Previously, it was considered either as “molecular fossil” or as only
a phosphorus and energy source providing the survival of microorganisms
under extreme conditions. These compounds are now known to also have
regulatory roles, and to occur in representatives of all kingdoms of
living organisms, participating in metabolic correction and control on
both genetic and enzymatic levels. Polyphosphate is directly involved in
the switching-over of the genetic program characteristic of the
exponential growth stage of bacteria to the program of cell survival
under stationary conditions, “a life in the slow line”. They participate
in many regulatory mechanisms occurring in bacteria:

They participate in the induction of rpoS, an RNA-polymerase subunit
which is responsible for the expression of a large group of genes
involved in adjustments to the stationary growth phase and many
stressful agents.

They are important for cell motility, biofilms formation and virulence.

Polyphosphates and exopolyphosphatases
participate in the regulation of the levels of the stringent response
factor, guanosine 5'-diphosphate 3'-diphosphate (ppGpp), a second
messenger in bacterial cells.

Polyphosphates participate in the formation of channels across the
living cell membranes. The above channels formed by polyphosphate and
poly-b-hydroxybutyrate with Ca2+ are involved in the transport processes in a variety of organisms.

An important function of polyphosphate in microorganisms—prokaryotes
and the lower eukaryotes—is to handle changing environmental conditions
by providing phosphate and energy reserves. Polyphosphates are present
in animal cells, and there are many data on its participation in the
regulatory processes during development and cellular proliferation and
differentiation—especially inbone tissues and brain.

In humans polyphosphates are shown to play a key role in blood coagulation.Produced and released byplatelets[5]they activate Factor XII
which is essential for blood clot formation. Furthermore
platelets-derived polyphosphates activate blood coagulation factor XII
(Hageman factor) that initiates fibrin formation and the generation of a
proinflammatory mediator, bradykinin that contributes to leakage from the blood vessels and thrombosis.[6][7]

Abstract

Prokaryotes and eukaryotes synthesize long
chains of orthophosphate, known as polyphosphate (polyP), which form
dense granules
within the cell. PolyP regulates myriad cellular
functions and is often localized to specific subcellular addresses
through
mechanisms that remain undefined. In this study, we
present a molecular-level analysis of polyP subcellular localization in
the model bacterium, Caulobacter crescentus.
We demonstrate that biogenesis and localization of polyP is controlled
as a function of the cell cycle, which ensures regular
partitioning of granules between mother and
daughter. The enzyme polyphosphate kinase 1 (Ppk1) is required for
granule production,
colocalizes with granules, and dynamically
localizes to the sites of new granule synthesis in nascent daughter
cells. Localization
of Ppk1 within the cell requires an intact
catalytic active site and a short, positively-charged tail at the
C-terminus of
the protein. The processes of chromosome
replication and segregation govern both the number and position of
Ppk1/polyP complexes
within the cell. We propose a multi-step model
whereby the chromosome establishes sites of polyP coalescence, which
recruit
Ppk1 to promote the in situ synthesis of large
granules. These findings underscore the importance of both chromosome
dynamics
and discrete protein localization as organizing
factors in bacterial cell biology.